You could name the notes in different rules for those to publish and the ones not, and then use "note_file_pattern" option in site_config. Only files matched the pattern will be listed and visited.
For note files, please use "note_file_pattern" option in site_config. Place a capture in the regular expression, and the first capture group will be the part of the url.
For directories, please use "name" option in category_config.
Notes and categories are in file system order by default. You could rename files and directories with a numeric prefix (e.g. first.md, second.md, ...), and hide the prefix by "note_file_pattern" option in site_config.
Make a directory and marked with "resource.toml" file in it. And then images in that directory can be referenced by notes. See resource_config for details.
Currently only markdown is supported and recommended.
Files in other formats will be displayed as-is. Thus, you could use .txt file for plain text, or write HTML contents in a .html file.
.doc/.docx are planned to be supported.